01 October 2008

Nomenclature vs. Science

Recently, due to an electronic submission SNAFU, an unreviewed paper naming a new species was accidentally published online. The new species is a very interesting one, of much interest to those of us who study the general group that it belongs to. But, we find ourselves morally obligated to avoid public discussion of it, because its publication was inadvertent. Now we must wait for the ponderous phases of review and publication to take place before we can discuss what we already know. In essence, the process of nomenclature is impeding the process of science.

Does this seem backward? Why shouldn't we be able to discuss new data as soon as they are available? Nomenclature is essential to proper communication, but should it be allowed to slow the march of science?

More to the point, why does nomenclature even have the opportunity to impede science? Why would we even set up a system that allowed that to happen? Why can't we publish data as soon as it's available (perhaps with an efficient review process)? Why do we place nomenclature on such a high pedestal?

Well, really, it's just one aspect of nomenclature that is placed on a pedestal: priority. Whoever publishes a name for a specimen first gets to be the NAMER OF THE TAXON, and any Johnnies-come-lately are mere footnotes. For this reason, researchers must keep their data under wraps to avoid "claim jumps".

Of course, objectively, they don't have to. It's really just that we, as humans, assign some sort of importance to the coiners of names. Naming is power. Naming is awesome.

So, in essence, it is human egotism that allows nomenclature to hinder science. That's all.

As I see it, there are two solutions: 1) we stop caring so much about who names stuff and get on with our lives, or 2) we revise the system. Option #1 is the ideal, but, like so many ideals, it's pretty unrealistic. So what about option #2?

Well, here's an idea. What if the nomenclatural codes allowed "specimen claims"? That is, what if you could register a specimen as "yours to name" for a specific amount of time, after which someone else could challenge you for the claim? Then no new taxa dependent on those specimens (or on species typified by those specimens) could be named by someone else.

Here are a couple of possible "use cases" under this idea:

Use Case 1.—Early publication of scientific data, later publication of nomenclature.1) Researcher discovers specimen.2) Specimen is catalogued in an institution.3) Specimen is registered under the nomenclatural code's database. Researcher now has X amount of time to name taxa based on the specimen.4) Researcher publishes a preliminary report on the specimen, noting its registration information.5) Researcher spends more time assessing the relationships of the organism(s) represented by the specimen. Based on this, Researcher decides that the specimen represents a new species and also decides that a new clade should be named using that species as a specifier.6) Researcher names the new species, typified by the specimen, and the new clade in a publication which is published before X amount of time has passed.

Use Case 2.—Differing taxonomic opinions.1) Researcher A discovers specimen.2) Specimen is catalogued in an institution.3) Specimen is registered under the nomenclatural code's database. Researcher A now has X amount of time to name taxa based on the specimen.4) Researcher A publishes a preliminary report on the specimen, noting its registration information.5) Researcher A spends more time assessing the relationships of the organism(s) represented by the specimen. Based on this, Researcher A decides that it belongs to a preexisting species and decides to publish a paper assigning it to that species.6) Researcher B reads the preliminary report, and notes data that indicate that it may belong to a new species.7) Researcher B notes that Researcher A has a hold on naming taxa based on the specimen, and communicates with Researcher A, learning Researcher A's taxonomic opinion.8) Researcher B maintains disagreement, and decides to name a new species based on the specimen.9) Researcher B challenges Researcher A's claim, via the nomenclatural code's database.10) Researcher A relinquishes the claim.11) Researchers A and B publish their respective papers with their differing opinions.Alternate course of events.10) Researcher A maintains the claim.11) Researcher A publishes the paper placing the specimen in a preexisting species.12) The claim expires after X amount of time.13) Researcher B publishes a paper placing the specimen in a new species.

Use Case 3.—Renewal. 1) Researcher discovers specimen. 2) Specimen is catalogued in an institution. 3) Specimen is registered under the nomenclatural code's database. Researcher now has X amount of time to name taxa based on the specimen. 4) Researcher publishes a preliminary report on the specimen, noting its registration information. 5) Researcher spends more time assessing the relationships of the organism(s) represented by the specimen. Based on this, Researcher decides that it belongs to a new species and decides to publish a paper naming the new species.6) Writing the paper takes more time than expected. Researcher applies for an extension to the claim through the nomenclatural code's database.7) The extension is automatically approved, since nobody else has filed a challenge.8) Researcher publishes the paper naming the new species.Note that the current process is possible under this scheme. That is, the researcher can forego registration if they plan to keep the data under wraps until the new taxa are published. Registration simply allows the researcher to get the scientific data out ASAP.

It does optionally involve a few extra steps, but this scheme allows researchers to get their data out as quickly as possible, and then take some time in establishing the nomenclature. That seems like an eminently desireable outcome.

9 comments:

However, the manuscript in question contains two or three serious problems that peer-review should, and hopefully will, fix. This includes the question of whether the new specimen really represents a new taxon.

Well, under this system, I think more time could be devoted to taxonomic issues, without there being any sense of dread that someone was going to scoop you. Basically, get the observations out there ASAP in the form of a report (which wouldn't even require traditional publication--could just be freely circulating PDFs or whatnot) so that people can start discussing the science and the nomenclature. Then, once things are hashed out, publish more complete works on the science and the nomenclature.

So much of science is done behind secretive curtains for this very silly reason. It frustrates me to see people giving nomenclatural priority more importance than actual scientific discussion. I think establishing a formal system of taxonomic claims could abolish that, speeding up our process without sacrificing integrity (and perhaps improving it, with data being in the public eye for greater amounts of time).

I don't see how any of these suggestions would help given the current example. Up untill this time, and various other occassions, the old system works. This example stands out due to its contents and the debate considering the nomenclatural issues, but should be considered a loner, a glitch. A glitch does not perse mean something needs to be overhauled.

Oh, it's not just this. There's also the Heliocanthus/Rioarribasuchus debacle and many other cases. And beyond those situations, think of all the specimens that can't be openly discussed yet because someone is working on their nomenclature. I think a system of formal claims could get information out there faster, so more eyes could see it. Isn't that one of science's primary goals?

Not only do I think this is a great idea, it's also one of the only good solutions to the whole issue of science publications and the net.

Look, some very good opinions are posted online that could really have benefited the authors of sub-par papers, and a lot of them the handful of peer reviewers could not possibly have all considered.

I think the E*********x mistake and Nature pre-pub could have been a good move if no nomenclature was involved: almost in a blog format, with a comments section that could act sort of like the semi-pros on the DML do. The DML type discussions would be moved to pre-pub, the real peer review could take it into account, and papers would be better off. Plus we'd get to like, actually talk about what everybody and their mom already knows and drop the pointless pretense.

However, the manuscript in question contains two or three serious problems that peer-review should, and hopefully will, fix. This includes the question of whether the new specimen really represents a new taxon.

Everyone here probably reads the DML, but just in case, the version that accidentally got prepublished was the final submission. It had already been peer-reviewed. The mentioned problems (geological age, ontogenetic age, diagnosability as a new taxon) are still in the published version, which is now officially out.